The secretary of veterans affairs, David J. Shulkin, for a year enjoyed rare bipartisan support in Washington as he reformed his department, but now officials in the Trump administration are trying to replace him.

An email sent in December by Jake Leinenkugel, the White House senior adviser on veterans affairs, expressed frustration with Dr. Shulkin and listed ways to topple the leadership of his department once key legislation was passed.

The email was addressed to Camilo Sandoval, a former data manager for the Trump campaign who was given a political post at the department. In it, Mr. Leinenkugel, a former brewery executive, wrote that although he initially had a positive impression of the secretary, they had fallen out over staffing and policy issues.

Mr. Leinenkugel, who has an office in the department, proposed “solutions” in the email, including using a continuing investigation of the secretary’s travel to remove Dr. Shulkin’s chief of staff, Vivieca Wright Simpson; replacing the deputy secretary, Thomas G. Bowman, with Mr. Leinenkugel; and replacing Dr. Shulkin with a “strong political candidate.”

Dr. Shulkin, the only holdover from the Obama administration, expressed dismay in an interview on Wednesday over what he said seemed to be political appointees in his office working against him, saying that they were “trying to undermine the department from within.”

Career civil servants say the dispute has grown more heated than previous policy differences, and the agency’s headquarters, a block from the White House, is rived with infighting between the secretary’s supporters and opponents.

The department’s inspector general released a scathing report on Wednesday about a business trip Dr. Shulkin took to Britain and Denmark last year. The report said he spent much of the trip sightseeing and improperly accepted a gift of Wimbledon tickets; it also accused Ms. Wright Simpson of wrongdoing in connection with Dr. Shulkin’s wife’s airfare, which it said should not have been paid by the department.

Dr. Shulkin characterized the report as inaccurate and biased, but he said he would reimburse the government for his wife’s airfare and pay for the tennis tickets.

Mr. Leinenkugel’s suggested replacement for Dr. Shulkin would be likely to spark controversy: Michael J. Kussman, a former under secretary who has been associated with Concerned Veterans of America, a group funded largely by the billionaire conservative activists Charles G. Koch and David H. Koch that advocates shifting spending on veterans’ health care to the private sector.

It is not clear whether the president supports the move. The Department of Veterans Affairs referred questions about its leadership, the tensions in the department and Mr. Leinenkugel’s email to the White House, which declined to comment.

The fight over the leadership of the department is part of a long-running battle over how to deliver health care to the nation’s veterans. The department currently operates its own health system, with more than 1,200 hospitals and clinics across the country where about nine million veterans receive treatment at little or no cost to them. Some conservatives, including some advisers to the White House, favor gradually dismantling that system and allowing veterans to choose to receive taxpayer-subsidized care from private doctors instead.

Veterans’ groups have overwhelmingly opposed that idea. But Mr. Trump promised during his election campaign that “vets will have the right to go to a V.A. facility or the right to see a private doctor or clinic of their choice — whatever is fastest or best for the vet.”

Policymakers in both parties have said that offering that kind of unrestricted choice between the public system and private providers would be too expensive. They have generally favored a more measured approach that would allow the department to approve the use of private care when waiting times are too long at veterans’ hospitals. Dr. Shulkin has also backed this plan.

Dr. Shulkin said in the interview that he was determined to remain in his post. Though one lawmaker called for his resignation in the wake of the travel report, others were cordial to Dr. Shulkin at a budget hearing Thursday morning and did not bring up the report.

He said he was investigating a number of political appointees in his department for misconduct and possible removal. On Thursday, he spoke directly to the White House chief of staff, John F. Kelly, about concerns that political appointees were trying to undermine his agency, according to department officials.

“If there are people here who don’t want the V.A. to succeed, I want them out,” Dr. Shulkin said in the interview.

Dr. Shulkin was an unexpected but popular choice for secretary. After the 2016 election, Mr. Trump considered several critics of the department as possible nominees to head the agency. But to the relief of most veterans’ organizations, he chose Dr. Shulkin, a moderate who headed the agency’s health care system under President Barack Obama.

Since then, Mr. Trump has repeatedly praised Dr. Shulkin. At a bill signing in June, he said the secretary did not have to worry about hearing Mr. Trump’s old reality-show catchphrase, “You’re fired.”

“We’ll never have to use those words on our David,” Mr. Trump said, pointing his finger at the secretary like a pistol. “We will never use those words on you, that’s for sure.”

But in recent months, some of the president’s appointees have felt betrayed by what they see as backtracking at the department on access to privately provided health care, and have moved to oust Dr. Shulkin.

“He has shown total disdain for the White House,” said one White House official, who was not authorized to discuss the matter. “This isn’t ideological; it is just what the president wants. He wants veterans to have choice.” The official said that current legislation to fund privately provided care was more restrictive than rules during the Obama administration.

In December, according to congressional staff members, political appointees in the department quietly bypassed the secretary to advance legislation that would open the way for more privately provided health care for veterans. The bill was introduced by Senator Jerry Moran, Republican of Kansas, who has received substantial campaign donations from the Koch brothers.

Turmoil at the department seems to be growing. Last week The Washington Post quoted unnamed White House officials who said Mr. Bowman, the deputy secretary, would soon be fired as a “warning shot” to “knock Shulkin down a peg or two” for not pushing harder for privatization.

In the interview, Dr. Shulkin said he had spoken to President Trump, and was told there were no plans to fire Mr. Bowman. He attributed the Post article to opponents trying to sow disarray.

He said he was worried that his chief of staff’s email account might have been hacked, and was investigating the matter.

In another sign of division, John Ullyot, a former top Trump campaign official who now runs the press office, told staff members in an email on Wednesday that reporters’ requests for comment should not be forwarded to the secretary or deputy secretary; instead, he would be referring them all to the White House.

The move forced Dr. Shulkin to do much of his communication with the media over the travel investigation on his personal cellphone.

A version of this article appears in print on , on Page A23 of the New York edition with the headline: V.A. Secretary Says White House Officials Are Trying to Force Him Out. Order Reprints | Today’s Paper | Subscribe